WASHINGTON — A top official of the American Cancer Society has resigned in part because of concern over some of the organization’s fund-raising partnerships.

The official, Dr. Otis W. Brawley, an executive vice president and chief medical officer, resigned his post late last week after 11 years at the society. His departure was largely attributed to his dismay over some commercial partnerships, including with Herbalife International, the controversial supplements company, people close to him said.

While he would not comment publicly, others said that he had become uncomfortable with the society’s growing reliance on donations from businesses with questionable health credentials that he and others suspect are seeking to burnish their images.

“It’s personally difficult and certainly for many in the organization it’s difficult as well,” Dr. Lichtenfeld said.

Such donations and fund-raising partnerships have become more important in recent years as the organization’s fund-raising has declined. Fund-raising income has gone down every year since its peak of just over $ 1 billion in 2007. In 2017, donations reached only $ 736 million, although the society made up for some of the loss by selling properties.

Critics in and outside the 105-year-old organization have also protested its recent partnerships with Long John Silver’s, a seafood chain best known for its batter-fried fish; and Tilted Kilt, a sports pub showcasing “Kilt Girls” in skimpy red plaid.

And Herbalife International has had a troubled history. The company donated $ 250,000 directly to the cancer society, and in October, started selling pink water bottles, that are co-branded with both the American Cancer Society and the Herbalife logo. Proceeds from the sales all go to the cancer society.

“These water bottles are really a good way for people to show their support,” said Sharon Byers, the society’s chief marketing officer. “Our intent with all of our partnerships is to generate as much revenue as we can to achieve our mission.”

In 2014, the Food and Drug Administration told Herbalife to take down a YouTube video that featured a former F.D.A. official implying that the agency approved weight loss shakes and other supplements.

“The company is too controversial historically,” said Arthur Caplan, director of medical ethics at the New York University School of Medicine. “It has a very non-illustrious history with regulatory bodies, association with a product of controversial and most likely dubious merit, and is not where the cancer society wants or ought to be.”

The Herbalife Facebook page shows both the cancer society and the company’s logo, with the phrase, “Working Together to Make the World Healthier and Happier and Free from Breast Cancer.” It does carry a disclaimer noting the cancer society does not endorse Herbalife products.

Dr. Caplan said the disclaimer isn’t enough. “Some people are going to think that there’s an implicit endorsement,” he said, “either because they don’t look at the website or they just see the bottle and presume a partnership.”

Historically, the cancer society’s revenue was heavily reliant on walks, including Relay for Life and Making Strides Against Breast Cancer, said Michael Reich, a spokesman for the organization. But during the past decade, he said, donations patterns have changed and walks, in particular, have become less popular.

“Because A.C.S.’s walks generated so much revenue and were such a large part of our portfolio, our declines were much more pronounced than some other organizations,” Mr. Reich said. “We have been re-engineering and diversifying our revenue portfolio, and partnerships are playing a key role. This takes time to build, but we are making tremendous progress.”

Ms. Byers, the cancer society’s chief marketing officer, said the organization does not form alliances with tobacco companies, but other than that, assesses each company individually.

Mr. Reich also defended the arrangement with the Tilted Kilt.

“I can tell you that A.C.S. is proud of the partnership with Tilted Kilt, too,” Mr. Reich said. “We do not yet have a plan for 2019, but we would certainly work with them again.”

Responding to internal criticism about the Tilted Kilt, Mr. Reich said, “We know we’re taking some risks. Not every partnership or initiative is for everyone.”

Janet Wilt, marketing director for the restaurant chain, said she was proud the company was a donor.

“Cancer is a disease that has touched all of our lives and it does not discriminate based on who you are or where you work,” she said in an email. “Frankly, we are disappointed people are offended by any organization supporting efforts toward finding a cure.”

The cancer society is not the only patient advocacy group struggling to expand its donor base without becoming tainted by associations with other groups.

A Boston University study two years ago identified scores of patient advocacy groups and other health organizations, including the American Heart Association and the American Diabetes Association, that accepted research funding from soda companies.

One of the cancer society’s new donors, Long John Silver’s, was the subject of criticism for its use of trans fats, which it has since dropped. James P. O’Reilly, the company’s chief executive, notes that the restaurant now offers healthier choices, among them baked shrimp and cod and grilled salmon, and is expanding its grilled selections on the menu.

“Long John Silver’s and its franchisees are proud to stand with the many millions of American families who battle cancer every day,” Mr. O’Reilly said in an email.

Jonathan H. Marks, associate professor of bioethics, humanities and law at Pennsylvania State University, pointed to the partnership’s conflicting messages.

“The partnership with Long John Silver’s undermines the integrity of the American Cancer Society,” Dr. Marks said. “The American Cancer Society’s website encourages readers to prepare fish and poultry by baking, broiling or poaching rather than by frying or charbroiling. But the society is partnering with a fast food company whose leading menu items are fried. Integrity requires consistency.”

Dr. Brawley, 59, said he was not able to discuss the terms of his departure. Members of the society said he also had concerns about the administration of its landmark program to make cancer drugs available at lower cost in Africa.